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Open Access Highly Accessed Research article

Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes

Dong Li12, Yiran Guo2, Haojing Shao2, Laurent C Tellier23, Jun Wang23, Zhonghuai Xiang1 and Qingyou Xia14*

Author Affiliations

1 The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China

2 BGI-Shenzhen, Shenzhen 518083, China

3 Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark

4 Institute of Agronomy and Life Sciences, Chongqing University, Chongqing 400030, China

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BMC Evolutionary Biology 2010, 10:81  doi:10.1186/1471-2148-10-81

Published: 24 March 2010

Abstract

Background

Mitochondria are a valuable resource for studying the evolutionary process and deducing phylogeny. A few mitochondria genomes have been sequenced, but a comprehensive picture of the domestication event for silkworm mitochondria remains to be established. In this study, we integrate the extant data, and perform a whole genome resequencing of Japanese wild silkworm to obtain breakthrough results in silkworm mitochondrial (mt) population, and finally use these to deduce a more comprehensive phylogeny of the Bombycidae.

Results

We identified 347 single nucleotide polymorphisms (SNPs) in the mt genome, but found no past recombination event to have occurred in the silkworm progenitor. A phylogeny inferred from these whole genome SNPs resulted in a well-classified tree, confirming that the domesticated silkworm, Bombyx mori, most recently diverged from the Chinese wild silkworm, rather than from the Japanese wild silkworm. We showed that the population sizes of the domesticated and Chinese wild silkworms both experience neither expansion nor contraction. We also discovered that one mt gene, named cytochrome b, shows a strong signal of positive selection in the domesticated clade. This gene is related to energy metabolism, and may have played an important role during silkworm domestication.

Conclusions

We present a comparative analysis on 41 mt genomes of B. mori and B. mandarina from China and Japan. With these, we obtain a much clearer picture of the evolution history of the silkworm. The data and analyses presented here aid our understanding of the silkworm in general, and provide a crucial insight into silkworm phylogeny.